Sequential activation of oncogenes and inactivation of tumor suppressor and DNA repair genes causes human cancers. The activation and inactivation of these cancer genes can be mutations or epigenetic modification such as methylation of CpG islands and chromatin modification. My researches center on integrating biological knowledge, genome sequences, and high-throughput experiments to identify genes and genetics elements that are important for the cancer development. Positional cloning and candidate cloning of cancer genes. We mapped a tumor suppressor gene locus to an 800-kb interval on human chromosome 13q12.11 for esophageal squamous cell carcinoma (ESCC). Two genes, ML-1 and RNF6, are located within this 800-kb interval. We analyzed both genes for the presence of mutations in 24 ESCC primary tumors and 16 tumor cell lines by directly sequencing the PCR products that were amplified from each exon. No mutation was detected in ML-1. In contrast, three somatic mutations in the RNF6 gene were detected in the ESCC primary tumors and one mutation was also found in a tumor cell line. Identification of multiple somatic mutations in RNF6 suggests that RNF6 is a potential tumor suppressor gene involved in the pathogenesis of ESCC. Genome-wide analysis of allelic gene expression and genomic imprinting. Variations in gene sequence and expression underlie much of human complex diseases and phenotypic variation in behaviors. Despite the known biological roles of differential allelic gene expression resulting from X chromosome inactivation and genomic imprinting, a large-scale analysis of allelic gene expression in human is lacking. We examined allele-specific gene expression of 1063 transcribed single nucleotide polymorphisms (SNPs) using Affymetrix HuSNP oligo arrays. Among the 602 genes that were heterozygous and expressed in kidney or liver tissues from seven individuals, 326 (54%) showed preferential expression of one allele in at least one individual, and 170 of those showed greater than 4-fold difference between the two alleles. The allelic variation has been confirmed by real-time quantitative PCR experiments. Some of these 170 genes are known to be imprinted, such as SNRPN, IPW, HTR2A, and PEG3. Most of the differentially expressed genes are not in known imprinting domains but instead are distributed throughout the genome. Our studies demonstrate that variation of gene expression between alleles is common, and understanding this variation will play a critical role in study complex diseases such as cancers. Methylation and chromatin analysis of genes in human cancers. To study the role of methylation of CpG islands in the regulation of genes involved in human cancers, we selected a list of 271 genes known to be important in human cancers. Eighty of 271 cancer genes have CpG islands in the promoter regions and 31 of these genes were assayed for methylation status in 35 pairs of cancer and normal samples. We found that BRCA2, HCK, LCK, RAB2L, and REBL had significant increases in the methylation of CpG islands in tumor samples. The McNemar test was used to test for the presence of methylation in tumor but absent in the matched normal sample vs. methylation in normal sample but absent in the matched tumor. The results indicated that methylation of BRCA2 and LCK are specifically increased in tumors compared to the matched normal samples. We are currently developing high throughput methods to analyze whole genome DNA methylation and chromatin structure.